GTEx RNA-Seq Visualizations

2013-09-21

I created three visualizations of RNA-Seq data from the GTEx project (version 2013-03-21). They're powered by JBrowse, the WashU Epigenome Browser, and canvasXpress.

(At some point, these links broke and I haven't had time to fix them.)

JBrowse Genome Browser#

GTEx JBrowse IGF2

View expression of each coding nucleotide in the human genome (hg19).

A nucleotide's expression level is the sum of Gencode v12 transcript RPKMs. The transcript levels were quantified by the GTEx team using Flux Capacitor. If you have RNA-Seq data, do not use Flux Capacitor. Instead, you should use RSEM or Cufflinks.

WashU Epigenome Browser#

GTEx Wash U Epigenome Browser

View the expression of Gencode v12 transcripts across 23 human tissues.

Heatmap#

GTEx heatmap IGF2

View expression of all Gencode v12 transcripts for a chosen gene.